http://www.copasi.org/tiki-forums_rss.php?ver=2 Fri, 10 Sep 2010 15:20:39 +0100 Tiki CMS/Groupware via FeedCreator 1.7.2.1 http://www.copasi.org/img/CopasiRSS-Alpha.png http://www.copasi.org/tiki-view_articles.php en-us webmaster@copasi.org http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=963 antony Tue, 07 Sep 2010 15:44:33 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=956 B B -> C C -> Then, I set species A to type assignment using expression to create a time trigger for species changes: IF(t LE 4, t, 0.0) where globalA is a global Quantity. At that point at parameter estimation, I run into the following warning message: CSteadyState (1): The model is explicitly time dependent. Therefore, the calculation of a steady state is not very meaningful. How should I interpret this warning? Are essential steady state calculations prevented and thus a correct parameter estimation prevented? Should I in general avoid explicitly time dependent models as the one above? Ideally, species A should act as reaction type for t]]> Simon Tue, 31 Aug 2010 11:51:12 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=947 acarbo Wed, 25 Aug 2010 12:29:32 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=945 ds_siRNA{Trap} ds_siRNA{Trap} = ds_siRNA{Cytosol} decay: ds_siRNA{Cytosol} -> a) single-compartment rate constant The rate constant for the decay reaction (ds_siRNA{Cytosol} ->) is assumed to be ln(2) divided by the halftime of an RNA-aptamer in 10% FCS. Can I use this value (3.47e+2 /h) directly in my model? b) multi-compartment rate constant The rate constants for the two multi-compartment reactions have units fmol/h. I am not sure, how I can use my experimentally derived rate constants with units of 1/h. Do I have to multiply them by the volume of the compartment that contains the reactant(s)? Thanks, Simon]]> Simon Wed, 25 Aug 2010 09:52:39 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=944 Joerg Mon, 23 Aug 2010 09:16:39 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=942 Conor Fri, 13 Aug 2010 15:26:24 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=940 Joerg Tue, 10 Aug 2010 14:57:02 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=938 Joerg Tue, 10 Aug 2010 12:56:31 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=932 0 and epsC]]> mederer Mon, 02 Aug 2010 11:43:38 +0100 http://www.copasi.org/tiki-view_forum_thread.php?forumId=1&comments_parentId=918 Waheed Tue, 27 Jul 2010 21:00:39 +0100